@ Az :
about the first instance of the "you're clueless" that was quite the contrary : every objective fact was saying that Misato was lying to him :
- "14 years have passed" : but Asuka looks exactly the same, and what proves me that this chick is really Toji's sister 14 years older?
- "Rei is no more" : cue Rei appearing one minute later piloting an almost perfect copy of EVA-00
Of course we know that something is fishy because we saw Earth turned red during operation US, we saw NGE and EoE and all the scenes between Gendo and SEELE and Kozo to know that he's a bastard with his own agenda that includes the end of the world, we saw all the hints that Rei and Yui are somehow related(like the diner between her and Gendo in 2.0)
But Shinji didn't saw any of it, and objectively what makes more sense : that 14 years have passed but for some reason Asuka hasn't changed and that Rei in EVA-00 isn't Rei in EVA-00, or simply that Misato is lying to him? Worst, she also admitted that now she's in an organization whose goal is to destroy NERV, but didn't had the time to explain that NERV are now the bad guys and that the Angels are no more, remember that one of the first things he asks to Rei Q when he goes to visit her in her "room" is "Why is Misato fighting Father instead of the Angels?", for him the Angels are still around and NERV is still trying to protect the world.
Like I said, at the moment Mark.09 appeared short of killing or restraining him, nothing would have prevented Shinji from getting out, simply because he don't have enough information and that everything points that Misato is lying.
Now for the second time, I agree that he should have been more suspicious about Kaworu's plan, if only because he didn't explained to him what those wo spears were exactly
going to do and thus why having two of the same screws completely the plan. Personally I think that Kaworu did it on purpose because his plan did include Instrumentality and that Shinji would be against it, but he thinks that it's nonetheless the only path for Shinji's happiness.
But OTOH he has seen truly insane things : the fact he stayed 14 tanged inside his EVA, a giant cyborg skeleton bird used as a giant flying flagship, the world turned to core material, giant headless zombies Evas, the Moon crashed on Earth with its own atmosphere, core-like grid and giant bloodstains while spinning widely on he surface, the fact Rei is a clone and witnessing dozen of severed heads of other clones, or the giant fucking mouth
that grew on Earth's surface...
From here are spears that can terraform the world back into an inhabitable shape that far-fetched? Hell Kaworu could have proposed time travel and I'm sure that most of the audience would have bought it!
Besides Shinji has always been someone passive, never really searching for people's motives or details about why he's asked to do something, as seen with his conversation with Misato in 1.11 where she asked him why he didn't asked what the hell was that giant thing(Sachiel), or lampshaded by Ritsuko during his VR training.
That's a big flaw he always had, that made him more easily manipulable, and that's something he will need to work on in Final if he ever hopes to become a better person.
Another on like you said is his extreme stubbornness once he made up his mind(like when he resigned after Bardiel), but he has been shown to be able to change his mind if the right arguments are presented to him, we saw an instance of that in each movies :
- in 1.0 when Misato showed him Lilith, explaining why they need him to pilot and protect Tokyo-3
- in 2.0 when he witnessed Rei being eaten by Zeruel, showing that running away won't make his problems disappear and that other people still can suffer from the consequences of his choices
- in 3.0 when he decided to never pilot again, until Kaworu asked him to trust him and go pilot one last time to save the Lilin, and made him trust him by removing the DSS Choker to put it himself
It's possible that Shinji was so desperate and insane that he wouldn't have listened to Asuka had she explained to him why he shouldn't touch those spears, but she could have at least tried, and that would have made her completely entitled to beat the shit out of him and go on full-assault, but by jumping to conclusions that he wouldn't listen to her, she passed for an enraged berserker who contributed to bring Shinji's extremely embrittled mind to the breaking point where he would pull out the spears whatever Kaworu told him.
And I'm sure that it was all according to Gendo's plan.
Now I'm not saying hat Shinji is totally blameless in this, even though Gendo drove him half-insane and exploited his flaws, Shinji is still the one who is at the biggest fault for triggering 4I, what I'm saying is that Asuka and Kaworu had too their part in it, albeit smaller.
And that's was I call this fight a shared Idiot Ball moment, because it would have been needed is that at least one of the three acted rationally to defuse this whole situation, or at least give it a chance to be defused, yet no one did.
And in the end Gendo is the great victor.